This preliminary report details the results of looking for pathway enrichment in each of the groups of genes produced by hierarchical clustering of the drug perturbations. I’ve cut the the data into 25, but this value can be changed if we decide on a different value. Otherwise, this analysis focuses on enriched pathways in the MSigDB database. Specifically, this analysis uses the Hallmark segment from: https://www.gsea-msigdb.org/gsea/msigdb.

As for this report, the panel on the left is sorted by the number of dark kinases in the cluster and displays both the number of pathway hits and dark kinases in the cluster. The number of each cluster is arbitrary. The entry for each cluster displays the kinases associated with the cluster along with the number of non-kinases genes. Below this table are the pathways that passed the enrichment analysis at the 0.01 false discovery rate level. I also corrected for running this analysis for all 25 clusters.

Overall Enrichment Stats

Overall, 44 pathways are enriched in at least one of the following clusters. Of these pathways 6 are only hit once. The following pathways are seen in two or more clusters:

Num: 12 (Pathways: 14 DK: 19)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (19) CAMK1D, CAMKV, CDKL3, DYRK1B, LMTK2, LMTK3, MAP3K15, MAPK15, MARK1, MKNK1, NEK5, PIK3C2B, PIP5K1B, SBK1, SCYL2, STK3, TESK2, TSSK1B, VRK3
Light Kinase (46) ACVR1C, ACVR2A, ACVRL1, ANKK1, BMP2K, BMX, CAMK2B, CAMK4, CDK9, CSF1R, DAPK1, DAPK2, DCLK1, EPHA6, EPHB2, EPHB3, FGFR1, FGFR2, FGFR3, FGFR4, FLT4, HCK, ITK, JAK2, KALRN, KSR1, KSR2, MAP2K3, MAP2K6, MAP4K1, MAPK10, MAPK11, MAST1, MATK, PI4KAP2, PRKCG, PRKCZ, PRKD2, PTK2, RPS6KA3, SGK2, SRPK2, STK26, STYK1, TAF1L, TXK
Non-kinase Count 1748
label pval fdr signature geneset overlap hits
HALLMARK_APICAL_JUNCTION 0.0e+00 0.0e+00 1813 200 31 ACTN2,ADAM23,AMIGO1,ATP1A3,CADM2,CALB2,CD209,CD34,CD86,CDH1,CDH15,CDH3,CNTN1,DHX16,DSC3,ICAM2,JAM3,KCNH2,LAYN,MAPK11,NECTIN2,NFASC,NRXN2,PARD6G,PPP2R2C,PTK2,SLC30A3,SYMPK,TJP1,TRO,VCAN
HALLMARK_SPERMATOGENESIS 0.0e+00 1.0e-07 1813 135 22 ACE,ALOX15,CAMK4,CHRM4,CNIH2,CRISP2,DCC,DDX25,DMRT1,GAD1,GSG1,GSTM3,JAM3,MAP7,MLF1,NOS1,SCG3,SEPTIN4,STAM2,STRBP,TNNI3,TUBA3C
HALLMARK_ALLOGRAFT_REJECTION 0.0e+00 1.0e-07 1813 200 27 ACHE,ACVR2A,CD1D,CD3D,CD40,CD74,CD86,CDKN2A,CRTAM,GPR65,IL11,IL12A,IL16,IL2RB,IL7,INHBB,ITGAL,ITK,JAK2,MAP4K1,NOS2,PRKCG,RPL3L,STAB1,STAT4,UBE2D1,WAS
HALLMARK_ESTROGEN_RESPONSE_LATE 0.0e+00 1.0e-07 1813 200 27 AFF1,ANXA9,CACNA2D2,CDH1,CYP26B1,DHRS2,DNAJC1,EMP2,FGFR3,IGSF1,JAK2,KCNK5,KLK10,KLK11,LSR,LTF,MOCS2,NPY1R,OLFM1,PDLIM3,PLAC1,PRKAR2B,S100A9,SLC1A4,SLC29A1,SULT2B1,TMPRSS3
HALLMARK_COMPLEMENT 0.0e+00 2.0e-07 1813 200 26 ACTN2,ATOX1,CLU,CPM,CR2,F5,FCN1,GCA,GRB2,HNF4A,HPCAL4,ITGAM,JAK2,KLK1,KLKB1,LGMN,LTF,MMP13,PIK3R5,PLA2G4A,PLAT,S100A9,SCG3,SH2B3,SPOCK2,WAS
HALLMARK_KRAS_SIGNALING_DN 1.0e-07 7.0e-07 1813 200 25 ABCG4,C5,CAMK1D,CLSTN3,CPEB3,CYP39A1,DCC,FGFR3,HSD11B2,IGFBP2,KCND1,KCNMB1,KCNN1,KLK7,NOS1,NR6A1,RYR1,SIDT1,SLC30A3,SLC5A5,SLC6A14,TAS2R4,TCF7L1,TFCP2L1,TNNI3
HALLMARK_IL2_STAT5_SIGNALING 1.1e-06 6.0e-06 1813 199 23 ABCB1,AHR,CD83,CD86,CST7,EOMES,ETFBKMT,FAM126B,GALM,GPR65,GUCY1B1,HUWE1,IL1R2,IL2RB,IL3RA,ITGA6,ITIH5,LRRC8C,MAP6,SELL,TLR7,TNFRSF8,TNFSF10
HALLMARK_ESTROGEN_RESPONSE_EARLY 1.2e-06 6.0e-06 1813 200 23 AFF1,ANXA9,CALB2,CYP26B1,DHRS2,ENDOD1,INHBB,JAK2,KAZN,KCNK5,KLK10,NPY1R,OLFM1,PDLIM3,PODXL,RAB17,REEP1,SLC1A4,SULT2B1,SYBU,TBC1D30,TMPRSS3,UGCG
HALLMARK_INFLAMMATORY_RESPONSE 1.2e-06 6.0e-06 1813 200 23 ACVR2A,ADGRE1,AHR,CCRL2,CD40,CD70,CYBB,FFAR2,IL2RB,LAMP3,NMUR1,NPFFR2,OPRK1,P2RX7,PIK3R5,PTAFR,PTGER4,SELL,SEMA4D,SLC28A2,STAB1,TNFSF10,TNFSF15
HALLMARK_MYOGENESIS 1.2e-06 6.0e-06 1813 200 23 ACHE,ACTN2,CAMK2B,CLU,CNN3,DAPK2,EIF4A2,EPHB3,FKBP1B,GNAO1,KCNH2,KLF5,MAPRE3,MYL2,NCAM1,NOS1,PTGIS,REEP1,RYR1,SLN,SPDEF,SPTAN1,TNNT2
HALLMARK_HEDGEHOG_SIGNALING 4.1e-06 1.9e-05 1813 36 9 ACHE,CRMP1,GLI1,HEY2,NKX6-1,NRP2,SCG2,SLIT1,TLE3
HALLMARK_INTERFERON_GAMMA_RESPONSE 1.4e-05 5.4e-05 1813 200 21 CD38,CD40,CD74,CD86,CIITA,IL2RB,IL7,ITGB7,JAK2,OASL,PELI1,PLA2G4A,SAMHD1,SLAMF7,ST3GAL5,STAT4,TDRD7,TNFSF10,TOR1B,TRAFD1,ZNFX1
HALLMARK_KRAS_SIGNALING_UP 1.4e-05 5.4e-05 1813 200 21 ABCB1,ACE,CBL,EPHB2,EVI5,FLT4,GPRC5B,GUCY1A1,IL33,KIF5C,MAP4K1,MAP7,MMD,PIGR,PLAT,SCG3,TMEM100,TMEM176B,TNNT2,TOR1AIP2,TPH1
HALLMARK_HEME_METABOLISM 4.5e-05 1.6e-04 1813 200 20 ACSL6,ADD2,ATG4A,BMP2K,BTRC,CDR2,ENDOD1,MAP2K3,MPP1,PSMD9,RAP1GAP,RBM38,RCL1,SLC30A10,SLC66A2,SPTA1,SPTB,TMCC2,TSPAN5,XK

Num: 11 (Pathways: 26 DK: 14)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (14) CDK19, DSTYK, HIPK3, LRRK1, MAP3K10, MARK4, NEK11, PIP4K2C, PIP5K1C, RPS6KC1, SBK3, SRPK3, STK38L, TTBK2
Light Kinase (32) AAK1, ABR, ACVR1, BRD2, CAMK2D, CSNK1D, DGKD, EIF2AK3, FRK, GSK3B, HK1, ILK, INSR, JAK1, LATS2, MAP2K2, MAP3K8, MAPK1, MAPKAPK2, MST1R, MYLK3, MYLK4, NRBP1, NUAK1, PEAK1, PI4K2A, PINK1, SIK3, TAOK3, TGFBR1, TRPM7, ULK1
Non-kinase Count 1183
label pval fdr signature geneset overlap hits
HALLMARK_CHOLESTEROL_HOMEOSTASIS 0.0e+00 0.0e+00 1229 74 20 ACAT2,ACSS2,ACTG1,CTNNB1,CYP51A1,EBP,ETHE1,FDFT1,FDPS,HMGCR,HMGCS1,IDI1,LGALS3,LSS,NSDHL,S100A11,SC5D,SCD,STARD4,TP53INP1
HALLMARK_MYOGENESIS 0.0e+00 0.0e+00 1229 200 27 ACSL1,APOD,APP,ATP6AP1,CHRNB1,COL6A2,DTNA,FDPS,FOXO4,GAA,GABARAPL2,HDAC5,ITGA7,ITGB1,LPIN1,MYL6B,MYO1C,NQO1,PC,PDE4DIP,PDLIM7,SCD,SIRT2,SORBS1,SVIL,TAGLN,TSC2
HALLMARK_MITOTIC_SPINDLE 0.0e+00 0.0e+00 1229 199 26 ABI1,ABR,AKAP13,ARHGAP10,ARHGAP5,ARHGEF12,ARL8A,CAPZB,CDC42,CDC42EP2,CSNK1D,CYTH2,DST,DYNC1H1,KIF3C,KIFAP3,MARK4,NEDD9,NOTCH2,OPHN1,PALLD,RABGAP1,RASAL2,SPTBN1,STK38L,WASL
HALLMARK_ANDROGEN_RESPONSE 0.0e+00 0.0e+00 1229 100 18 ABHD2,APPBP2,ARID5B,DHCR24,HMGCR,HMGCS1,IDI1,INSIG1,ITGAV,MYL12A,NCOA4,PLPP1,PTPN21,SCD,SLC38A2,TMEM50A,ZBTB10,ZMIZ1
HALLMARK_HEME_METABOLISM 0.0e+00 0.0e+00 1229 200 23 ALDH6A1,ARHGEF12,BLVRB,CLCN3,CTNS,CTSB,DMTN,FN3K,HTATIP2,KHNYN,LAMP2,LPIN2,LRP10,MBOAT2,MOSPD1,NCOA4,OPTN,PC,PGLS,PPP2R5B,SDCBP,SLC22A4,YPEL5
HALLMARK_FATTY_ACID_METABOLISM 0.0e+00 0.0e+00 1229 158 20 ACAT2,ACOT8,ACOX1,ACSL1,DECR1,DHCR24,EHHADH,ERP29,GLUL,HADHB,HMGCS1,HSD17B11,IDH1,IDI1,INMT,NSDHL,RETSAT,SERINC1,TP53INP2,VNN1
HALLMARK_APOPTOSIS 0.0e+00 0.0e+00 1229 161 20 APP,CTNNB1,CYLD,DCN,DNAJC3,EBP,HGF,HMOX1,IGF2R,IGFBP6,LGALS3,MADD,NEDD9,PPP2R5B,PSEN1,RETSAT,SC5D,SMAD7,SQSTM1,TIMP2
HALLMARK_IL2_STAT5_SIGNALING 0.0e+00 0.0e+00 1229 199 22 AHNAK,ANXA4,CAPG,CD81,CDC42SE2,COL6A1,CYFIP1,FURIN,IGF2R,ITGAV,KLF6,MAP3K8,MAPKAPK2,MYO1C,PLPP1,RABGAP1L,SERPINB6,SMPDL3A,SNX14,SNX9,SWAP70,TWSG1
HALLMARK_XENOBIOTIC_METABOLISM 0.0e+00 0.0e+00 1229 200 22 ACOX1,ADH5,AKR1C3,AQP9,BLVRB,CDA,DHRS7,HES6,HMOX1,HRG,HSD17B2,IDH1,LPIN2,NQO1,PC,PINK1,PMM1,PROS1,RETSAT,SLC12A4,UPB1,VNN1
HALLMARK_APICAL_JUNCTION 0.0e+00 1.0e-07 1229 200 21 ACTG1,ARHGEF6,BAIAP2,CAP1,CD276,CERCAM,CTNNA1,EXOC4,GNAI2,INSIG1,ITGB1,MADCAM1,MDK,MPZL1,MSN,MYL12B,RRAS,SGCE,SIRPA,THBS3,WASL
HALLMARK_BILE_ACID_METABOLISM 1.0e-07 5.0e-07 1229 112 15 ABCA9,ACSL1,AQP9,ATXN1,CYP8B1,DHCR24,HSD17B11,IDH1,IDI1,OPTN,PAOX,PEX6,PHYH,PRDX5,RETSAT
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 1.0e-07 6.0e-07 1229 200 20 CALD1,CAPG,COL6A2,DAB2,DCN,DST,FAP,FBLN5,FZD8,ITGAV,ITGB1,LAMC1,LRP1,MATN3,NOTCH2,PLOD2,PMP22,SGCB,TAGLN,VIM
HALLMARK_PEROXISOME 3.0e-07 1.1e-06 1229 104 14 ACOT8,ACOX1,ACSL1,ATXN1,CLN8,DHCR24,EHHADH,FDPS,HSD17B11,IDH1,IDI1,PEX6,PRDX5,RETSAT
HALLMARK_COMPLEMENT 6.0e-07 2.1e-06 1229 200 19 APOC1,C1S,CDA,CP,CPQ,CTSB,CTSD,FCER1G,GNAI2,GNB2,LAMP2,LGALS3,LRP1,PCSK9,PRCP,PSEN1,RHOG,S100A13,TIMP2
HALLMARK_MTORC1_SIGNALING 6.0e-07 2.1e-06 1229 200 19 ATP6V1D,CCNG1,CXCR4,CYP51A1,DHCR24,EBP,GSK3B,HMGCR,HMGCS1,IDH1,IDI1,INSIG1,PGM1,PLOD2,SC5D,SCD,SQSTM1,STARD4,TXNRD1
HALLMARK_TGF_BETA_SIGNALING 7.0e-07 2.2e-06 1229 54 10 ACVR1,CTNNB1,FURIN,NCOR2,RAB31,RHOA,SKIL,SMAD7,SPTBN1,TGFBR1
HALLMARK_UV_RESPONSE_DN 3.0e-06 8.7e-06 1229 144 15 ANXA4,ATP2B4,ATXN1,DAB2,FBLN5,INSIG1,LAMC1,MAP1B,NOTCH2,PMP22,PTPN21,SDC2,SMAD7,WDR37,ZMIZ1
HALLMARK_WNT_BETA_CATENIN_SIGNALING 7.3e-06 2.0e-05 1229 42 8 ADAM17,CTNNB1,FRAT1,FZD8,HDAC5,NCOR2,NUMB,WNT5B
HALLMARK_COAGULATION 8.5e-06 2.2e-05 1229 138 14 APOC1,C1S,CPQ,CTSB,FURIN,GNB2,HRG,LAMP2,LRP1,MST1,PROS1,S100A13,SIRT2,USP11
HALLMARK_HYPOXIA 1.1e-05 2.5e-05 1229 200 17 CAVIN3,CP,CXCR4,DCN,DTNA,EFNA1,FOSL2,GAA,HK1,HMOX1,KLF6,KLHL24,NAGK,PGM1,PRDX5,SDC2,SLC2A5
HALLMARK_OXIDATIVE_PHOSPHORYLATION 1.1e-05 2.5e-05 1229 200 17 ACAT1,ALDH6A1,ATP6AP1,ATP6V0E1,ATP6V1C1,ATP6V1D,ATP6V1E1,COX6A1,COX6C,CYB5R3,DECR1,HADHA,HADHB,IDH1,PHYH,RETSAT,RHOT1
HALLMARK_PROTEIN_SECRETION 2.5e-05 5.6e-05 1229 96 11 CD63,CLCN3,DST,GNAS,IGF2R,LAMP2,MAPK1,MON2,RAB9A,SNAP23,STX7
HALLMARK_ADIPOGENESIS 4.0e-05 8.0e-05 1229 200 16 ACOX1,APLP2,CD151,COX6A1,DECR1,DHRS7,ESYT1,IDH1,ITGA7,PGM1,PHYH,RETSAT,RNF11,SORBS1,SPARCL1,TANK
HALLMARK_ESTROGEN_RESPONSE_EARLY 4.0e-05 8.0e-05 1229 200 16 ABHD2,BLVRB,DYNLT3,FAM102A,FDFT1,FRK,KDM4B,MED13L,NCOR2,NRIP1,RAB31,SH3BP5,SLC37A1,SNX24,SVIL,TTC39A
HALLMARK_P53_PATHWAY 4.0e-05 8.0e-05 1229 200 16 APP,BAIAP2,CCNG1,CD81,CTSD,CTSF,EPS8L2,FGF13,HMOX1,MXD4,PHLDA3,PMM1,RALGDS,RETSAT,RPS27L,SERTAD3
HALLMARK_KRAS_SIGNALING_UP 1.4e-04 2.7e-04 1229 200 15 ADAM17,ADGRL4,APOD,CCSER2,CSF2RA,CXCR4,FCER1G,GALNT3,GPNMB,LY96,MTMR10,PTPRR,RABGAP1L,SPARCL1,ZNF277

Num: 7 (Pathways: 3 DK: 11)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (11) CAMKK1, MAST2, NEK1, NEK4, PAN3, PHKG2, PIP5K1A, TAOK1, TESK1, TLK1, ULK4
Light Kinase (20) ADPGK, BAZ1A, BAZ1B, CAMK2A, CDK3, CSK, DDR2, DGKE, GRK2, HSPB8, MAP3K6, MAPK7, MLKL, PASK, PI4KB, PIK3C3, SLK, STK4, TPTEP2-CSNK1E, TTN
Non-kinase Count 868
label pval fdr signature geneset overlap hits
HALLMARK_G2M_CHECKPOINT 0 0e+00 899 200 24 AMD1,ATRX,CASP8AP2,CHMP1A,CTCF,CUL5,E2F1,E2F2,GINS2,HNRNPD,KIF5B,LMNB1,MCM3,NASP,PDS5B,RBL1,RBM14,SFPQ,SMARCC1,SMC2,SRSF2,SS18,TMPO,TRA2B
HALLMARK_MITOTIC_SPINDLE 0 1e-07 899 199 19 ALMS1,ARFGEF1,ATG4B,CDK5RAP2,CLIP1,CNTRL,CTTN,EPB41L2,HOOK3,KIF1B,KIF5B,LMNB1,NF1,PCNT,RALBP1,SMC3,STAU1,TLK1,WASF1
HALLMARK_E2F_TARGETS 0 1e-07 899 200 19 CTCF,DEK,HNRNPD,LMNB1,LUC7L3,MCM3,MCM4,MSH2,NASP,PCNA,PDS5B,POLD3,SMC3,SPC24,SRSF2,TCF19,TMPO,TRA2B,UBR7

Num: 2 (Pathways: 13 DK: 10)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (10) BRSK1, CDK11B, CDK16, CSNK1G3, MARK3, PHKG1, RIOK1, RIOK2, RPS6KL1, VRK2
Light Kinase (22) CASK, CDK8, CSNK2A1, DGKG, EIF2AK2, FLT1, GAK, HUNK, MAP3K4, MAPK9, MARK2, PAK4, PDPK2P, PIM1, PLK2, PRKAA1, RPS6KB1, SGK3, TBK1, TEX14, TRIB3, TRIM33
Non-kinase Count 983
label pval fdr signature geneset overlap hits
HALLMARK_MYC_TARGETS_V1 0.0e+00 0.0e+00 1015 200 57 ABCE1,ACP1,CANX,CCT2,CCT3,CCT4,CCT5,CCT7,CNBP,COPS5,DDX18,DDX21,EIF2S1,EIF2S2,EIF3J,EIF4H,EPRS1,ETF1,GLO1,GNL3,HSP90AB1,ILF2,KARS1,MYC,NOLC1,NPM1,PRDX4,PSMA4,PSMA6,PSMB3,PSMD14,PSMD3,RACK1,RAD23B,RPL14,RPL18,RPL34,RPL6,RPLP0,RPS10,RPS2,RPS3,RPS5,RPS6,RSL1D1,SF3A1,SNRPB2,SRSF1,SRSF3,SRSF7,TARDBP,TCP1,TUFM,U2AF1,XPO1,XPOT,XRCC6
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 0.0e+00 0.0e+00 1015 113 27 ALDH18A1,ASNS,ATF3,CEBPG,CXXC1,DDX10,DNAJB9,EIF2S1,EXOSC1,FKBP14,GOSR2,HERPUD1,MTHFD2,MTREX,NFYA,NOLC1,NOP14,NPM1,PDIA6,PSAT1,RPS14,SDAD1,SERP1,SLC7A5,SRPRA,TARS1,XPOT
HALLMARK_MTORC1_SIGNALING 0.0e+00 0.0e+00 1015 200 32 ARPC5L,ASNS,BCAT1,CANX,CCT6A,COPS5,CTH,DDIT3,DDX39A,EIF2S2,EPRS1,ETF1,GCLC,HSPA4,IMMT,MTHFD2,PHGDH,PNO1,PSAT1,PSMA4,PSMD13,PSMD14,PSMG1,RPN1,SERP1,SHMT2,SLC7A5,TBK1,TCEA1,TFRC,TRIB3,UFM1
HALLMARK_MYC_TARGETS_V2 0.0e+00 0.0e+00 1015 58 14 BYSL,DDX18,DUSP2,GNL3,IMP4,MYC,NDUFAF4,NOLC1,NOP2,NPM1,RABEPK,RRP12,TFB2M,WDR43
HALLMARK_UV_RESPONSE_UP 0.0e+00 3.0e-07 1015 158 17 ASNS,ATF3,BTG3,CDC34,CEBPG,CXCL2,DDX21,EIF2S3,FOSB,MARK2,MSX1,NUP58,PRPF3,RPN1,TARS1,TFRC,TMBIM6
HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0e+00 3.0e-07 1015 200 19 ATF3,BTG3,CCL5,CD44,CXCL2,CXCL3,DUSP2,EIF1,FOSB,GADD45A,GFPT2,HBEGF,HES1,IFNGR2,KLF10,MYC,PLK2,TNC,ZFP36
HALLMARK_E2F_TARGETS 8.0e-07 4.7e-06 1015 200 17 AK2,ASF1A,DDX39A,EIF2S1,EZH2,MTHFD2,MYC,NOLC1,PPM1D,PRDX4,PRIM2,SRSF1,TFRC,TIPIN,XPO1,XRCC6,ZW10
HALLMARK_G2M_CHECKPOINT 8.0e-07 4.7e-06 1015 200 17 DDX39A,EZH2,H2BC12,KATNA1,MNAT1,MYC,NOLC1,NUP98,PAFAH1B1,PRIM2,PRMT5,RAD23B,SLC7A5,SRSF1,UPF1,WRN,XPO1
HALLMARK_P53_PATHWAY 8.0e-07 4.7e-06 1015 200 17 AEN,ATF3,DDIT3,GADD45A,HBEGF,OSGIN1,PLK2,PPM1D,RACK1,RAD9A,RPL18,RPL36,RPS12,SEC61A1,SERPINB5,TGFA,TRIB3
HALLMARK_APOPTOSIS 5.9e-06 2.8e-05 1015 161 14 ANXA1,ATF3,BCL10,BTG3,CD14,CD44,CTH,DAP3,DDIT3,DFFA,EREG,ETF1,GADD45A,PMAIP1
HALLMARK_ANDROGEN_RESPONSE 6.3e-06 2.8e-05 1015 100 11 ADAMTS1,CENPN,DNAJB9,GNAI3,HOMER2,HSD17B14,LMAN1,PGM3,RRP12,SEC24D,XRCC6
HALLMARK_PROTEIN_SECRETION 2.7e-05 1.1e-04 1015 96 10 ARFGAP3,COPB1,COPB2,COPE,GOLGA4,GOSR2,LMAN1,RAB2A,SEC24D,ZW10
HALLMARK_ALLOGRAFT_REJECTION 6.7e-05 2.6e-04 1015 200 14 ABCE1,BCAT1,BCL10,CCL5,EIF3J,EREG,HLA-A,IFNGR2,NPM1,RPL39,RPL9,RPS19,RPS3A,RPS9

Num: 1 (Pathways: 7 DK: 9)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (9) ADCK1, ADCK5, CDC42BPG, COQ8B, MAST3, NEK9, PRAG1, STK32A, TAOK2
Light Kinase (28) BCR, BRD3, CKMT1A, CKMT1B, EIF2AK1, EPHA7, EPHB6, ERBB4, KDR, LIMK1, MAP3K13, MAP3K5, MAP4K2, MINK1, PRKACA, PRKCA, PRKCH, PRKX, PTK2B, ROCK2, RPS6KA2, SGK1, STK11, STK38, TGFBR2, TNK2, TRIM66, UHMK1
Non-kinase Count 1088
label pval fdr signature geneset overlap hits
HALLMARK_ESTROGEN_RESPONSE_LATE 0.0e+00 3.0e-07 1125 200 21 ABCA3,AGR2,ALDH3A2,ARL3,CD9,CELSR2,HR,IDH2,ITPK1,LLGL2,PLAAT3,RPS6KA2,SCARB1,SCNN1A,SGK1,SLC9A3R1,SNX10,TIAM1,TPD52L1,TST,UNC13B
HALLMARK_APICAL_JUNCTION 8.0e-07 1.3e-05 1125 200 18 CDH8,CLDN11,CLDN9,CRAT,EVL,IRS1,ITGA3,JUP,LDLRAP1,MAP4K2,MYH10,NRTN,PECAM1,SDC3,TAOK2,TMEM8B,VCL,YWHAH
HALLMARK_GLYCOLYSIS 8.0e-07 1.3e-05 1125 200 18 AGRN,ALDH7A1,ALG1,ARPP19,B3GAT3,BPNT1,CHST12,CHST2,CLDN9,COG2,CYB5A,GLCE,LHPP,NDST3,PKP2,PYGB,SDC3,XYLT2
HALLMARK_BILE_ACID_METABOLISM 1.5e-06 1.9e-05 1125 112 13 ABCA3,ABCD2,ABCD3,AMACR,CROT,GSTK1,IDH2,LIPE,MLYCD,NR1H4,PEX1,PEX7,SLC22A18
HALLMARK_ESTROGEN_RESPONSE_EARLY 3.4e-06 3.4e-05 1125 200 17 ABCA3,ABLIM1,ADCY1,ADCY9,ARL3,BCL11B,CELSR2,GJA1,HR,ITPK1,PLAAT3,RPS6KA2,SCARB1,SCNN1A,SLC9A3R1,TIAM1,TPD52L1
HALLMARK_PEROXISOME 2.4e-05 2.0e-04 1125 104 11 ABCD2,ABCD3,CRAT,DLG4,GSTK1,IDH2,ITGB1BP1,MLYCD,MVP,PEX2,YWHAH
HALLMARK_ADIPOGENESIS 5.4e-05 3.8e-04 1125 200 15 ADIPOQ,CAVIN1,COL4A1,CRAT,ELOVL6,FZD4,GPHN,LIFR,LIPE,LPCAT3,LPL,REEP6,SCARB1,SLC66A3,TST

Num: 4 (Pathways: 11 DK: 9)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (9) CDK11A, CDK12, CDKL1, COQ8A, CSNK1G1, CSNK2A2, NEK7, PDIK1L, TLK2
Light Kinase (18) ARAF, AURKB, BUB1, CDK1, CDK2, CHEK1, DGKZ, GSK3A, GTF2F1, IRAK3, MASTL, MELK, NEK2, PAK1, PAK2, PLK4, SRPK1, YES1
Non-kinase Count 1129
label pval fdr signature geneset overlap hits
HALLMARK_E2F_TARGETS 0.0e+00 0.0e+00 1156 200 49 ANP32E,ATAD2,AURKB,BRCA2,BRMS1L,CCNB2,CDC25A,CDK1,CENPM,CHEK1,CNOT9,CTPS1,DCK,DEPDC1,ESPL1,GINS4,GSPT1,HMGB2,HMMR,ILF3,ING3,IPO7,KIF2C,KPNA2,MCM7,MELK,MMS22L,NUP153,NUP205,ORC6,PHF5A,PLK4,POLE,POP7,PSMC3IP,RACGAP1,RAD1,RAD21,RAD51AP1,RAN,RNASEH2A,RPA2,SLBP,SNRPB,TOP2A,TUBB,UBE2T,UNG,USP1
HALLMARK_G2M_CHECKPOINT 0.0e+00 0.0e+00 1156 200 49 AURKB,BRCA2,BUB1,CCNA2,CCNB2,CCNT1,CDC25A,CDC27,CDC6,CDK1,CENPA,CHEK1,CUL1,CUL3,CUL4A,DKC1,DR1,E2F3,ESPL1,GSPT1,HMGN2,HMMR,HNRNPU,ILF3,INCENP,KIF2C,KMT5A,KPNA2,KPNB1,NEK2,NSD2,NUP50,NUSAP1,ODF2,ORC6,PLK4,POLE,PRC1,RACGAP1,RAD21,RAD54L,RPA2,TENT4A,TNPO2,TOP2A,TPX2,TRAIP,TROAP,UBE2C
HALLMARK_MYC_TARGETS_V1 0.0e+00 0.0e+00 1156 200 38 CCNA2,CDK2,COX5A,CTPS1,CUL1,CYC1,EEF1B2,EIF4A1,EIF4G2,GSPT1,HNRNPA3,HNRNPU,IFRD1,KPNA2,KPNB1,MCM7,MRPL9,PABPC1,PHB2,PSMA1,PSMA7,PSMB2,PSMC6,PSMD8,PWP1,RAN,RNPS1,RPL22,RRM1,RRP9,SET,SNRPA,SNRPA1,SRPK1,UBA2,USP1,VBP1,VDAC1
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0e+00 0.0e+00 1156 200 28 ABCB7,ACO2,ATP5F1B,ATP5MG,ATP5PB,ATP6V1G1,COX5A,CS,CYC1,ECI1,GRPEL1,HSD17B10,IDH3B,MFN2,MRPL15,MRPS15,MRPS30,NDUFA9,NDUFS3,NDUFS7,NDUFS8,PHB2,SLC25A5,TIMM10,TIMM50,UQCRC2,UQCRH,VDAC1
HALLMARK_MITOTIC_SPINDLE 0.0e+00 0.0e+00 1156 199 23 BIN1,BRCA2,BUB1,CCNB2,CDC27,CDK1,CEP57,CEP72,CKAP5,CNTROB,ESPL1,INCENP,KIF2C,NEK2,NUSAP1,PCGF5,PPP4R2,PRC1,RAB3GAP1,RACGAP1,RASA2,TOP2A,TPX2
HALLMARK_MTORC1_SIGNALING 0.0e+00 0.0e+00 1156 200 22 ABCF2,ACTR3,BUB1,CDC25A,CYB5B,EEF1E1,GLA,GMPS,IFRD1,NFKBIB,NFYC,NUP205,PSMA3,PSMB5,PSMC2,PSMC6,RRP9,SEC11A,SLC7A11,SORD,SSR1,UNG
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 1.0e-07 4.0e-07 1156 113 15 CNOT2,CNOT6,DKC1,EIF4A1,EXOSC10,EXOSC4,EXOSC5,EXOSC9,PAIP1,RRP9,SEC11A,SLC30A5,SRPRB,SSR1,TATDN2
HALLMARK_MYC_TARGETS_V2 1.0e-07 5.0e-07 1156 58 11 EXOSC5,GRWD1,NIP7,PES1,PLK4,PPAN,PPRC1,PUS1,RRP9,SORD,UNG
HALLMARK_DNA_REPAIR 2.3e-06 1.2e-05 1156 150 15 ADRM1,ALYREF,ARL6IP1,DDB1,ELL,ELOA,ERCC8,GTF2F1,NT5C3A,POLR3C,RAD51,RPA2,SF3A3,SNAPC5,TMED2
HALLMARK_PROTEIN_SECRETION 2.3e-06 1.2e-05 1156 96 12 ANP32E,AP1G1,AP2B1,ARCN1,ARFGEF2,CLTA,GLA,RAB14,RER1,SCAMP3,STX16,TMED2
HALLMARK_UV_RESPONSE_UP 8.5e-05 3.9e-04 1156 158 13 BID,CASP3,CDK2,CYB5B,DNAJA1,EIF5,GRPEL1,HNRNPU,KLHDC3,PARP2,PPIF,PPP1R2,PSMC3

Num: 3 (Pathways: 11 DK: 8)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (8) ADCK2, CAMKK2, CDK13, CSNK1G2, MAST4, NEK6, SCYL3, TP53RK
Light Kinase (16) ALPK1, CLK2, EGFR, MTOR, NLK, PDGFRA, PDK4, PIK3CG, PKN1, PKN2, ROR1, RYK, STK24, STK39, TBRG4, TEK
Non-kinase Count 876
label pval fdr signature geneset overlap hits
HALLMARK_KRAS_SIGNALING_UP 0.0e+00 0.0e+00 900 200 20 ALDH1A3,BIRC3,BTBD3,CA2,ETV1,FBXO4,GNG11,ITGBL1,LAPTM5,LAT2,LIF,MPZL2,PDCD1LG2,PLAU,PRRX1,PSMB8,RELN,RGS16,SCG5,TMEM158
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0e+00 1.0e-07 900 200 19 AIFM1,ATP5F1A,ATP5MC1,ATP5MC2,ATP5ME,ATP5PO,COX17,COX8A,FH,ISCU,MDH2,MRPS11,MTX2,NDUFA7,NDUFB6,NDUFS1,NDUFV1,PDK4,UQCRFS1
HALLMARK_DNA_REPAIR 6.0e-07 1.1e-05 900 150 14 CCNO,COX17,DDB2,ERCC1,GSDME,IMPDH2,MRPL40,NCBP2,NELFB,NELFE,POLR2G,POLR2I,SAC3D1,TAF9
HALLMARK_INTERFERON_ALPHA_RESPONSE 1.0e-05 1.3e-04 900 97 10 BATF2,CASP1,CMTR1,IFI44L,IFITM1,IRF2,MVB12A,PSMB8,PSMB9,TAP1
HALLMARK_XENOBIOTIC_METABOLISM 1.8e-05 1.8e-04 900 200 14 AHCY,ASL,CA2,CES1,CNDP2,DHPS,GCH1,GSS,IGFBP4,NINJ1,PDK4,PEMT,PSMB10,XDH
HALLMARK_FATTY_ACID_METABOLISM 3.2e-05 2.6e-04 900 158 12 ACSL4,ACSL5,ADSL,ALDH1A1,CA2,CYP4A11,FH,GCDH,GRHPR,MDH2,MGLL,PTPRG
HALLMARK_BILE_ACID_METABOLISM 3.7e-05 2.6e-04 900 112 10 ABCA6,ACSL5,ALDH1A1,EFHC1,GNPAT,LONP2,NEDD4,NR3C2,PEX12,SLC27A5
HALLMARK_IL2_STAT5_SIGNALING 7.3e-05 3.5e-04 900 199 13 AHCY,CA2,CCR4,IKZF2,IL18R1,IL1RL1,LIF,MUC1,NCS1,PDCD2L,RGS16,SYNGR2,UCK2
HALLMARK_ADIPOGENESIS 7.7e-05 3.5e-04 900 200 13 AIFM1,ATP5PO,COQ3,COX8A,ESRRA,MDH2,MGLL,MRAP,MTCH2,PEMT,QDPR,RMDN3,SQOR
HALLMARK_INFLAMMATORY_RESPONSE 7.7e-05 3.5e-04 900 200 13 CD82,GCH1,HAS2,IFITM1,IL18R1,LIF,MARCO,MEFV,RGS16,SGMS2,SRI,TLR3,TPBG
HALLMARK_INTERFERON_GAMMA_RESPONSE 7.7e-05 3.5e-04 900 200 13 BATF2,CASP1,CMTR1,GCH1,IFI44L,IRF2,NLRC5,PSMB10,PSMB8,PSMB9,SRI,TAP1,VCAM1

Num: 10 (Pathways: 6 DK: 7)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (7) BRSK2, CDK18, CDKL2, LTK, MAP3K14, STK31, STK33
Light Kinase (15) ACVR1B, AKT3, DAPK3, EPHA4, FES, FYN, GRK5, LCK, MAP3K9, MAP4K5, MERTK, NPR2, PRKG1, TNK1, TNNI3K
Non-kinase Count 714
label pval fdr signature geneset overlap hits
HALLMARK_GLYCOLYSIS 1.0e-07 2.9e-06 736 200 16 ARTN,CAPN5,CHPF2,CHST1,CITED2,COL5A1,G6PD,HS2ST1,LHX9,MERTK,P4HA1,P4HA2,PAM,SOX9,UGP2,VLDLR
HALLMARK_HYPOXIA 1.9e-06 4.7e-05 736 200 14 CITED2,COL5A1,FOXO3,LOX,P4HA1,P4HA2,PAM,PPARGC1A,STBD1,TMEM45A,TPST2,UGP2,VLDLR,XPNPEP1
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 9.8e-06 1.2e-04 736 200 13 APLP1,COL5A1,FBN1,FLNA,FUCA1,ID2,LOX,LUM,MAGEE1,MATN2,NID2,P3H1,RHOB
HALLMARK_KRAS_SIGNALING_UP 9.8e-06 1.2e-04 736 200 13 ADGRA2,BTC,CBX8,FUCA1,ID2,IGF2,MMP11,NAP1L2,PLVAP,RBP4,SLPI,SOX9,VWA5A
HALLMARK_ESTROGEN_RESPONSE_EARLY 4.7e-05 3.9e-04 736 200 12 ABAT,AQP3,KRT8,LRIG1,MAPT,P2RY2,RETREG1,SYNGR1,TJP3,TOB1,TUBB2B,WFS1
HALLMARK_HEME_METABOLISM 4.7e-05 3.9e-04 736 200 12 ACP5,AQP3,BSG,DAAM1,FOXO3,IGSF3,MGST3,P4HA2,PICALM,SLC30A1,TNRC6B,TNS1

Num: 18 (Pathways: 8 DK: 7)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (7) CDC42BPB, CDK15, ICK, NEK8, NRBP2, STK32C, STK36
Light Kinase (21) ABL1, AXL, DGKA, EIF2AK4, ERBB2, IGF1R, IKBKB, IKBKE, MAP2K5, MAP3K11, MAP3K12, MAPK3, MYLK, NPR1, PIK3CB, PRKD1, ROS1, STK16, STRADA, TRIO, ULK2
Non-kinase Count 976
label pval fdr signature geneset overlap hits
HALLMARK_ADIPOGENESIS 0.0e+00 0.0e+00 1004 200 23 ACADS,ACLY,ADCY6,C3,CAVIN2,CD36,COQ9,CPT2,CYP4B1,ETFB,GPAM,HADH,ITSN1,JAGN1,MARC2,MCCC1,MYLK,PHLDB1,PPM1B,SCP2,SDHC,SLC25A1,VEGFB
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.0e+00 1.0e-07 1004 200 20 ACTA2,ADAM12,ANPEP,CDH6,COL12A1,COL1A1,COL5A2,DKK1,FBLN1,FSTL1,GAS1,LAMA3,MGP,MYLK,PCOLCE,PMEPA1,SNTB1,TGFBR3,TPM1,TPM4
HALLMARK_ESTROGEN_RESPONSE_EARLY 0.0e+00 5.0e-07 1004 200 19 AKAP1,ALDH3B1,AR,ASB13,CA12,CALCR,CCN5,CELSR1,ESRP2,FKBP5,IGF1R,MINDY1,MYOF,NAV2,OPN3,SLC1A1,SLC26A2,SYT12,TMEM164
HALLMARK_UV_RESPONSE_DN 0.0e+00 5.0e-07 1004 144 16 AGGF1,APBB2,ATRN,COL1A1,COL5A2,DMAC2L,EFEMP1,ERBB2,IGF1R,MAP2K5,MIOS,NFIB,PIAS3,RXRA,SMAD3,TGFBR3
HALLMARK_P53_PATHWAY 2.0e-07 1.5e-06 1004 200 18 AK1,BLCAP,BTG2,CCND3,CDKN2B,DGKA,ERCC5,F2R,HEXIM1,ITGB4,PLXNB2,RXRA,STEAP3,TAX1BP3,TP53,TP63,VDR,ZBTB16
HALLMARK_BILE_ACID_METABOLISM 1.7e-05 1.4e-04 1004 112 11 ABCA8,ABCD1,AR,HSD3B7,NUDT12,PEX11G,PEX13,PXMP2,RXRA,SCP2,SULT1B1
HALLMARK_FATTY_ACID_METABOLISM 2.0e-05 1.5e-04 1004 158 13 ACADS,ACOT2,AUH,CD36,CPOX,CPT2,ECI2,HADH,HPGD,MAOA,RDH11,SDHC,SUCLG2
HALLMARK_ESTROGEN_RESPONSE_LATE 6.0e-05 3.7e-04 1004 200 14 ALDH3B1,ASCL1,CA12,CALCR,CCN5,DLG5,ETFB,FKBP5,IMPA2,MYOF,OPN3,PLXNB1,SERPINA3,SLC26A2

Num: 19 (Pathways: 0 DK: 7)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (7) CDK17, CLK3, DYRK2, HIPK1, RIOK3, SCYL1, STK19
Light Kinase (23) ABL2, ATM, BRD4, BTK, CAMK2G, CLK1, FER, GRK7, HKDC1, LYN, MAP2K7, MAP4K4, MAPK6, MAPK8, MYLK2, RPS6KA5, SIK1, SIK1B, SMG1, STK10, STK35, TYRO3, WEE1
Non-kinase Count 744
label pval fdr signature geneset overlap hits

Num: 5 (Pathways: 9 DK: 6)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (6) ALPK3, CDKL5, NEK10, PAK3, PAK6, WNK3
Light Kinase (13) CKB, DGKB, DMPK, EPHA1, EPHA5, FGR, LIMK2, LRRK2, PKDCC, PRKCD, PRKY, RAF1, TIE1
Non-kinase Count 629
label pval fdr signature geneset overlap hits
HALLMARK_ESTROGEN_RESPONSE_LATE 0.0e+00 1.0e-07 648 200 17 CISH,CKB,CLIC3,CPE,CXCL12,ELOVL5,GPER1,PDCD4,PDZK1,SEMA3B,SERPINA5,SLC22A5,SLC27A2,SLC2A8,ST6GALNAC2,TNNC1,TRIM29
HALLMARK_ESTROGEN_RESPONSE_EARLY 0.0e+00 2.0e-07 648 200 16 B4GALT1,CISH,CLDN7,CLIC3,CXCL12,ELOVL5,GFRA1,GREB1,KCNK15,OLFML3,PDZK1,PEX11A,SEMA3B,SLC22A5,SLC27A2,TSKU
HALLMARK_MYOGENESIS 0.0e+00 2.0e-07 648 200 16 ANKRD2,CASQ1,CAV3,CKB,COL15A1,COL3A1,DMPK,EFS,ENO3,LDB3,MB,MYOM1,PYGM,SPARC,TNNC1,TNNI2
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 1.0e-07 8.0e-07 648 200 15 BGN,BMP1,CADM1,COL1A2,COL3A1,COL8A2,CXCL12,EFEMP2,FBLN2,MMP2,MYL9,PCOLCE2,SPARC,TGFBI,WNT5A
HALLMARK_APICAL_JUNCTION 4.0e-07 3.5e-06 648 200 14 ACTG2,ALOX15B,B4GALT1,BMP1,CLDN7,GNAI1,GRB7,INPPL1,MMP2,MYL9,NLGN3,PIK3R3,TGFBI,VWF
HALLMARK_COMPLEMENT 4.0e-07 3.5e-06 648 200 14 APOBEC3G,C1R,CFB,CR1,CTSH,CTSS,DPP4,GATA3,MMP12,OLR1,PLSCR1,PRKCD,PRSS36,RAF1
HALLMARK_COAGULATION 2.1e-06 1.5e-05 648 138 11 APOC3,BMP1,C1R,CFB,CTSH,DPP4,MMP2,MMP7,OLR1,SPARC,VWF
HALLMARK_XENOBIOTIC_METABOLISM 2.5e-06 1.6e-05 648 200 13 ALDH3A1,ALDH9A1,APOE,CFB,CYP17A1,CYP2C18,CYP2E1,ELOVL5,FMO1,FMO3,PTGDS,SERPINA6,SLC35D1
HALLMARK_FATTY_ACID_METABOLISM 7.7e-06 4.3e-05 648 158 11 ACADL,ALDH3A1,ALDH9A1,AOC3,AQP7,CEL,ELOVL5,ENO3,FMO1,GPD1,SLC22A5

Num: 14 (Pathways: 16 DK: 6)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (6) CDK20, CLK4, DYRK3, DYRK4, NEK3, NUAK2
Light Kinase (12) ACVR2B, AURKC, BMPR1B, BRAF, CDK7, CSNK1E, MAP3K20, PIM3, PTK6, RIPK2, TRIB1, TRPM6
Non-kinase Count 536
label pval fdr signature geneset overlap hits
HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0e+00 0.0e+00 554 200 50 BHLHE40,BIRC2,BMP2,BTG1,CEBPB,CFLAR,CSF2,CXCL1,CXCL10,DDX58,DRAM1,ETS2,GADD45B,ICAM1,IFIH1,IFIT2,IL1A,IL1B,IL6,INHBA,IRF1,JAG1,KYNU,LAMB3,MSC,NFKB2,NFKBIA,NFKBIE,PER1,PHLDA2,PLAUR,PLEK,PNRC1,PTGS2,PTX3,RELB,RIPK2,SERPINB8,SOD2,SPSB1,STAT5A,TGIF1,TNFAIP2,TNFAIP3,TNFAIP8,TNIP1,TRAF1,TRIB1,VEGFA,ZC3H12A
HALLMARK_INTERFERON_GAMMA_RESPONSE 0.0e+00 0.0e+00 554 200 27 BTG1,CMPK2,CXCL10,DDX58,DHX58,GBP4,ICAM1,IDO1,IFIH1,IFIT1,IFIT2,IL6,IRF1,ISG15,NFKBIA,PARP12,PTGS2,RBCK1,RIPK2,RSAD2,SOCS1,SOD2,TNFAIP2,TNFAIP3,TXNIP,UPP1,WARS1
HALLMARK_KRAS_SIGNALING_UP 0.0e+00 0.0e+00 554 200 21 AVL9,BMP2,C3AR1,CSF2,CXCL10,ETS1,HDAC9,HSD11B1,IKZF1,IL1B,INHBA,NGF,PLAUR,PRDM1,PTGS2,RBM4,ST6GAL1,TNFAIP3,TRAF1,TRIB1,TSPAN1
HALLMARK_INTERFERON_ALPHA_RESPONSE 0.0e+00 0.0e+00 554 97 15 CMPK2,CXCL10,DHX58,GBP4,HLA-C,IFIH1,IFIT2,IRF1,ISG15,NUB1,PARP12,RIPK2,RSAD2,TXNIP,WARS1
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.0e+00 0.0e+00 554 200 18 CXCL1,FERMT2,FGF2,GADD45B,IL32,IL6,INHBA,LAMC2,MMP1,PDLIM4,PLAUR,PPIB,PTX3,SNAI2,TFPI2,TNFAIP3,TNFRSF12A,VEGFA
HALLMARK_INFLAMMATORY_RESPONSE 0.0e+00 0.0e+00 554 200 18 C3AR1,CSF3,CSF3R,CXCL10,GNA15,ICAM1,IL1A,IL1B,IL6,INHBA,IRF1,NFKBIA,NLRP3,PLAUR,RIPK2,RNF144B,SLC11A2,SLC7A2
HALLMARK_HYPOXIA 0.0e+00 1.0e-07 554 200 15 AMPD3,BHLHE40,BTG1,CCNG2,CDKN1B,DDIT4,ETS1,GCNT2,HOXB9,IL6,NR3C1,PLAUR,PNRC1,TNFAIP3,VEGFA
HALLMARK_APOPTOSIS 0.0e+00 2.0e-07 554 161 13 BMP2,CDKN1B,CFLAR,GADD45B,GNA15,IL1A,IL1B,IL6,IRF1,KRT18,SOD2,TNFRSF12A,TXNIP
HALLMARK_IL6_JAK_STAT3_SIGNALING 0.0e+00 3.0e-07 554 87 10 CSF2,CSF3R,CXCL1,CXCL10,IL1B,IL6,IRF1,LTBR,SOCS1,TNFRSF12A
HALLMARK_ALLOGRAFT_REJECTION 1.0e-07 3.0e-07 554 200 14 DYRK3,ELF4,ETS1,HCLS1,HDAC9,ICAM1,IL1B,IL6,INHBA,NCK1,NLRP3,RIPK2,SOCS1,WARS1
HALLMARK_IL2_STAT5_SIGNALING 2.7e-06 1.2e-05 554 199 12 BHLHE40,BMP2,CDCP1,CSF2,CXCL10,GADD45B,GBP4,GSTO1,NFKBIZ,SOCS1,TRAF1,XBP1
HALLMARK_P53_PATHWAY 2.8e-06 1.2e-05 554 200 12 BMP2,BTG1,CDH13,DDIT4,DRAM1,IL1A,KRT17,NUPR1,SOCS1,TXNIP,UPP1,ZFP36L1
HALLMARK_PROTEIN_SECRETION 1.2e-05 4.7e-05 554 96 8 ARF1,BET1,KRT18,OCRL,RAB5A,TMED10,TOM1L1,YIPF6
HALLMARK_COMPLEMENT 1.7e-05 5.9e-05 554 200 11 CDH13,CEBPB,CXCL1,IL6,IRF1,KYNU,L3MBTL4,PLAUR,PLEK,TFPI2,TNFAIP3
HALLMARK_CHOLESTEROL_HOMEOSTASIS 1.9e-05 6.2e-05 554 74 7 CPEB2,JAG1,PLAUR,PNRC1,PPARG,STX5,TNFRSF12A
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 4.0e-05 1.2e-04 554 113 8 ATF6,CEBPB,DDIT4,HYOU1,IFIT1,PDIA5,VEGFA,XBP1

Num: 9 (Pathways: 10 DK: 4)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (4) EEF2K, PKMYT1, PRPF4B, RSKR
Light Kinase (23) AKT1, ATR, BUB1B, CDC7, CHUK, CIT, EPHA3, FASTKD1, FASTKD2, FASTKD3, FASTKD5, GRK6, HASPIN, MAP3K7, PBK, PI4K2B, PLK1, PRKDC, RPS6KA1, STRADB, TRIM28, TTK, VRK1
Non-kinase Count 1112
label pval fdr signature geneset overlap hits
HALLMARK_E2F_TARGETS 0.0e+00 0.0e+00 1139 200 84 ASF1B,BARD1,BIRC5,BRCA1,BUB1B,CCNE1,CCP110,CDC20,CDCA3,CDCA8,CDKN3,CENPE,CIT,CKS1B,CKS2,CSE1L,DCLRE1B,DCTPP1,DLGAP5,DNMT1,DONSON,DSCC1,DUT,E2F8,EED,EXOSC8,GINS1,GINS3,H2AX,H2AZ1,HELLS,JPT1,KIF18B,KIF22,KIF4A,LBR,LIG1,LYAR,MAD2L1,MCM2,MCM5,MCM6,MKI67,MLH1,MRE11,MXD3,MYBL2,NCAPD2,NME1,NOP56,NUP107,ORC2,PA2G4,PAICS,PLK1,PNN,POLA2,POLD1,PPP1R8,PRKDC,PRPS1,PSIP1,PTTG1,RAD51C,RANBP1,RFC2,RFC3,RPA1,RPA3,RRM2,SMC1A,SMC6,SPAG5,SPC25,SSRP1,STMN1,SUV39H1,SYNCRIP,TACC3,TIMELESS,TK1,TRIP13,TUBG1,UBE2S
HALLMARK_G2M_CHECKPOINT 0.0e+00 0.0e+00 1139 200 60 BARD1,BIRC5,BUB3,CCNF,CDC20,CDC45,CDC7,CDKN3,CENPE,CENPF,CHAF1A,CKS1B,CKS2,DBF4,DTYMK,E2F4,EXO1,FANCC,FBXO5,H2AX,H2AZ1,H2AZ2,HIRA,JPT1,KIF11,KIF15,KIF20B,KIF22,KIF23,KIF4A,KNL1,LBR,MAD2L1,MCM2,MCM5,MCM6,MKI67,MTF2,MYBL2,NCL,NDC80,ORC5,PBK,PLK1,POLA2,POLQ,PRPF4B,PTTG1,SMC1A,SNRPD1,SRSF10,STIL,STMN1,SUV39H1,SYNCRIP,TACC3,TFDP1,TOP1,TTK,UBE2S
HALLMARK_MYC_TARGETS_V1 0.0e+00 0.0e+00 1139 200 58 APEX1,BUB3,C1QBP,CAD,CDC20,CDC45,CLNS1A,CSTF2,DHX15,DUT,EIF1AX,EIF3B,EIF4E,ERH,FBL,GOT2,H2AZ1,HDAC2,HNRNPC,HNRNPR,HPRT1,HSPD1,HSPE1,LSM7,MAD2L1,MCM2,MCM5,MCM6,NCBP1,NDUFAB1,NME1,NOP16,NOP56,ORC2,PA2G4,PHB,POLE3,PPM1G,PRDX3,PRPS2,PTGES3,RANBP1,RFC4,SERBP1,SNRPD1,SNRPD3,SNRPG,SRM,SSB,SSBP1,STARD7,SYNCRIP,TFDP1,TOMM70,TRIM28,TXNL4A,TYMS,UBE2L3
HALLMARK_MYC_TARGETS_V2 0.0e+00 0.0e+00 1139 58 21 DCTPP1,HSPD1,HSPE1,IPO4,LAS1L,MCM5,MPHOSPH10,MRTO4,MYBBP1A,NOC4L,NOP16,NOP56,PA2G4,PHB,PLK1,PRMT3,SLC19A1,SRM,TCOF1,UTP20,WDR74
HALLMARK_DNA_REPAIR 0.0e+00 0.0e+00 1139 150 28 BOLA2,CLP1,CSTF3,DUT,FEN1,GTF2A2,GTF2H3,GTF3C5,HPRT1,LIG1,NME1,POLA1,POLA2,POLD1,POLR1C,POLR2D,POLR2F,POLR2K,PRIM1,RFC2,RFC3,RFC4,RFC5,RPA3,SNAPC4,SSRP1,TYMS,UMPS
HALLMARK_MITOTIC_SPINDLE 0.0e+00 0.0e+00 1139 199 30 ANLN,ARAP3,BIRC5,CENPE,CENPF,CENPJ,CEP192,DLGAP5,ECT2,FBXO5,GEMIN4,KIF11,KIF15,KIF20B,KIF22,KIF23,KIF4A,KNTC1,NDC80,PIF1,PLEKHG2,PLK1,RHOT2,SASS6,SHROOM2,SMC1A,TTK,TUBA4A,TUBGCP3,TUBGCP5
HALLMARK_MTORC1_SIGNALING 0.0e+00 0.0e+00 1139 200 24 ADIPOR2,CACYBP,CCNF,CTSC,DHFR,FDXR,HPRT1,HSPD1,HSPE1,MCM2,MTHFD2L,NUFIP1,PDAP1,PITPNB,PLK1,POLR3G,PSME3,PSPH,RPA1,RRM2,STIP1,TUBA4A,TUBG1,UCHL5
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0e+00 0.0e+00 1139 200 22 ATP5PF,COX11,CYCS,DLAT,FXN,GOT2,IDH3A,LDHB,MRPL11,MRPL35,MRPS12,MRPS22,NDUFAB1,OPA1,POLR2F,PRDX3,RHOT2,SDHB,SDHD,TIMM17A,TOMM22,TOMM70
HALLMARK_UV_RESPONSE_UP 3.7e-06 2.1e-05 1139 158 15 AP2S1,CCNE1,CDC5L,CHRNA5,FEN1,FKBP4,H2AX,PDAP1,POLE3,POLG2,PPAT,RASGRP1,RFC4,STIP1,TUBA4A
HALLMARK_ADIPOGENESIS 6.2e-05 3.1e-04 1139 200 15 ADIPOR2,ATL2,ATP1B3,CHUK,CMBL,DHRS7B,DLAT,GPD2,IDH3A,NDUFAB1,PRDX3,PTCD3,SDHB,SLC19A1,SLC5A6

Num: 17 (Pathways: 10 DK: 4)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (4) OBSCN, STK17A, STK17B, TSSK4
Light Kinase (14) BLVRA, GRK3, GRK4, MAP3K1, MAPK13, MET, MYO3B, NTRK3, PDK3, PIK3CD, PRKCI, SNRK, SYK, TNIK
Non-kinase Count 379
label pval fdr signature geneset overlap hits
HALLMARK_INFLAMMATORY_RESPONSE 0.0e+00 0.0e+00 397 200 18 BDKRB1,CCL22,CD55,CX3CL1,EBI3,IL10,IRF7,ITGB3,LCP2,LDLR,MET,NOD2,P2RX4,PTPRE,SERPINE1,TIMP1,TNFAIP6,TNFSF9
HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0e+00 0.0e+00 397 200 16 BCL2A1,BCL6,FOS,FUT4,IL6ST,LDLR,NFIL3,NR4A3,PDLIM5,PTPRE,SAT1,SDC4,SERPINE1,SOCS3,TNFAIP6,TNFSF9
HALLMARK_COMPLEMENT 0.0e+00 0.0e+00 397 200 14 CASP4,CBLB,CD55,DOCK4,DOCK9,IRF7,LCP2,LTA4H,PDGFB,PDP1,PHEX,SERPINE1,SIRT6,TIMP1
HALLMARK_HYPOXIA 0.0e+00 1.0e-07 397 200 13 AKAP12,ANGPTL4,ERRFI1,FOS,ISG20,LARGE1,MAP3K1,NFIL3,PDGFB,PDK3,SDC4,SERPINE1,TGM2
HALLMARK_CHOLESTEROL_HOMEOSTASIS 1.0e-07 1.4e-06 397 74 8 DHCR7,ERRFI1,HSD17B7,LDLR,MVD,NFIL3,PDK3,SQLE
HALLMARK_UV_RESPONSE_DN 2.5e-06 2.1e-05 397 144 9 ADD3,CACNA1A,ICA1,ITGB3,LDLR,MET,PDLIM5,PIK3CD,SERPINE1
HALLMARK_ESTROGEN_RESPONSE_LATE 5.2e-06 3.3e-05 397 200 10 ADD3,CCNA1,DHCR7,FOS,IL6ST,ISG20,LARGE1,MAPK13,PTGES,TSPAN13
HALLMARK_INTERFERON_GAMMA_RESPONSE 5.2e-06 3.3e-05 397 200 10 CASP4,FGL2,HLA-B,IRF5,IRF7,ISG20,LCP2,SOCS3,TNFAIP6,TRIM25
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 3.6e-05 1.8e-04 397 200 9 EDIL3,ITGB3,MMP3,SAT1,SDC4,SERPINE1,SERPINE2,TGM2,TIMP1
HALLMARK_ESTROGEN_RESPONSE_EARLY 3.6e-05 1.8e-04 397 200 9 ADD3,DHCR7,FOS,GAB2,IL6ST,KRT15,MPPED2,PTGES,TGM2

Num: 21 (Pathways: 0 DK: 3)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (3) POMK, PSKH1, TSSK6
Light Kinase (14) CAMK1, CDK6, CHEK2, DCLK2, LATS1, MAPK12, MAPK14, MOK, PIK3R4, PRKG2, RPS6KA4, RPS6KB2, STK25, TYK2
Non-kinase Count 375
label pval fdr signature geneset overlap hits

Num: 8 (Pathways: 5 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) MKNK2, NIM1K
Light Kinase (5) DYRK1A, MAP3K2, PDK1, PRKAA2, TEC
Non-kinase Count 390
label pval fdr signature geneset overlap hits
HALLMARK_HYPOXIA 0.0e+00 0.00000 397 200 33 AK4,ALDOA,ANKZF1,BNIP3L,DPYSL4,EFNA3,ENO1,ENO2,ERO1A,F3,FAM162A,GAPDH,GLRX,GPI,IDS,IGFBP3,KLF7,LDHA,NDRG1,PDK1,PGF,PGK1,PLIN2,PPFIA4,PPP1R3C,RBPJ,RRAGD,SAP30,SLC2A3,SLC6A6,TPD52,TPI1,WSB1
HALLMARK_GLYCOLYSIS 0.0e+00 0.00000 397 200 27 ABCB6,AK4,ALDOA,ANG,ANKZF1,DPYSL4,EFNA3,EGLN3,ENO1,ENO2,ERO1A,FAM162A,GLRX,GNE,IGFBP3,LDHA,ME1,NOL3,PGK1,PKM,PLOD1,PPFIA4,RRAGD,SAP30,SPAG4,TALDO1,TPI1
HALLMARK_MTORC1_SIGNALING 0.0e+00 0.00000 397 200 18 AK4,ALDOA,EGLN3,ENO1,ERO1A,FADS1,GAPDH,GLRX,GPI,LDHA,ME1,MLLT11,PDK1,PGK1,PRDX1,SLC2A3,SLC6A6,TPI1
HALLMARK_PROTEIN_SECRETION 1.2e-05 0.00015 397 96 7 AP2M1,AP3S1,BNIP3,GBF1,SCAMP1,SEC31A,TPD52
HALLMARK_OXIDATIVE_PHOSPHORYLATION 3.6e-05 0.00036 397 200 9 ACADVL,BCKDHA,COX6B1,ETFA,GPI,LDHA,NDUFA6,NDUFA8,POR

Num: 13 (Pathways: 2 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) BCKDK, TBCK
Light Kinase (1) DDR1
Non-kinase Count 118
label pval fdr signature geneset overlap hits
HALLMARK_INTERFERON_ALPHA_RESPONSE 4.1e-06 0.00021 121 97 5 B2M,CXCL11,ELF1,IFI27,PSME1
HALLMARK_OXIDATIVE_PHOSPHORYLATION 1.0e-05 0.00025 121 200 6 ACADM,COX5B,HTRA2,NDUFB8,NQO2,TCIRG1

Num: 15 (Pathways: 0 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) PI4KA, RNASEL
Light Kinase (14) BMPR2, CDK5, EPHA10, FPGT-TNNI3K, JAK3, MAP2K4, PDGFRB, PDK2, PIK3C2A, PRKD3, PTK7, ROCK1, SPEG, TRIM24
Non-kinase Count 334
label pval fdr signature geneset overlap hits

Num: 16 (Pathways: 4 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) MAP3K21, STK40
Light Kinase (13) AURKA, CDK4, CSNK1A1, EPHA2, HK2, IRAK2, MAP2K1, MAPKAPK3, MAPKAPK5, PIM2, PLK3, TAF1, TRIB2
Non-kinase Count 573
label pval fdr signature geneset overlap hits
HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0e+00 0.0e+00 588 200 17 AREG,CCL20,DUSP4,DUSP5,FOSL1,IER2,IER5,IL15RA,IL23A,MAFF,MCL1,NAMPT,PANX1,PHLDA1,SLC16A6,SPHK1,TLR2
HALLMARK_IL2_STAT5_SIGNALING 0.0e+00 4.0e-07 588 199 15 BATF3,EMP1,ETV4,HK2,IL4R,MAFF,ODC1,PHLDA1,PNP,PRNP,PTRH2,SLC1A5,SPRED2,SPRY4,ST3GAL4
HALLMARK_KRAS_SIGNALING_UP 2.9e-05 3.6e-04 588 200 11 CCL20,DUSP6,EMP1,ETV4,ETV5,MALL,PLEK2,SNAP25,SPRY2,TRIB2,WDR33
HALLMARK_MYC_TARGETS_V1 2.9e-05 3.6e-04 588 200 11 CBX3,CDK4,EIF3D,G3BP1,IARS1,ODC1,PABPC4,POLD2,PSMD7,RUVBL2,YWHAE

Num: 20 (Pathways: 0 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) PKN3, TSSK3
Light Kinase (14) AKT2, BMPR1A, DGKH, DGKI, HIPK2, IRAK1, MAP3K3, MAP4K3, PDPK1, PIK3CA, RIPK1, SIK2, TRRAP, WNK1
Non-kinase Count 276
label pval fdr signature geneset overlap hits

Num: 22 (Pathways: 2 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) CSNK2A3, PRKACB
Light Kinase (3) DGKQ, ERBB3, RPS6KA6
Non-kinase Count 370
label pval fdr signature geneset overlap hits
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0e+00 0.0e+00 375 200 17 ATP5F1C,ATP5F1E,ATP5PD,COX7A2,COX7C,GPX4,NDUFB1,NDUFB5,OGDH,OXA1L,PDHB,SLC25A11,SLC25A20,TIMM8B,UQCR11,UQCRB,UQCRQ
HALLMARK_DNA_REPAIR 2e-07 5.8e-06 375 150 10 APRT,DAD1,GPX4,MPG,POLR2E,POLR3GL,RBX1,TAF10,TSG101,XPC

Num: 23 (Pathways: 1 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) CDC42BPA, CDK10
Light Kinase (2) FASTK, WNK4
Non-kinase Count 200
label pval fdr signature geneset overlap hits
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0 0 204 200 12 ATP5MC3,ATP5MF,COX15,COX7B,ECHS1,MRPL34,NDUFA2,NDUFA3,NDUFB7,NDUFS6,SDHA,UQCR10

Num: 24 (Pathways: 1 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) ALPK2, PXK
Light Kinase (4) BRDT, ERN1, MAK, PRKCE
Non-kinase Count 248
label pval fdr signature geneset overlap hits
HALLMARK_MTORC1_SIGNALING 1e-06 4.9e-05 254 200 9 DAPP1,GOT1,HSP90B1,HSPA5,NIBAN1,SDF2L1,SYTL2,USO1,YKT6

Num: 6 (Pathways: 1 DK: 1)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (1) CDK14
Light Kinase (3) AATK, OXSR1, RIPK4
Non-kinase Count 171
label pval fdr signature geneset overlap hits
HALLMARK_KRAS_SIGNALING_UP 7.4e-06 0.00037 175 200 7 CCND2,CFH,EPB41L3,GABRA3,ITGA2,ITGB2,SPP1

Num: 25 (Pathways: 0 DK: 0)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (0)
Light Kinase (2) EPHB4, SRC
Non-kinase Count 101
label pval fdr signature geneset overlap hits